Hi PC01,
The purpose of the JOBKEEPER-START-FNxx and JOBKEEPER-FINISH-FNxx pay categories is to notify the ATO 1) when an eligible employee has started receiving JobKeeper payments and 2) when an employee is no longer eligible and payments have ceased. Once you have reported the FN Start category for the employee, you only need to use the JobKeeper Top-Up category to record any payments being made until you are reporting the FN Finish category.
You may find this article helpful on managing JobKeeper payments in a pay run, and refer to this article for fixing any JobKeeper payment errors if required. Feel free to reply if you have further questions as I'm here to help.
-Kass
